Contacts of the strand formed by residues 327 - 333 (chain H) in PDB entry 5LS6
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 327 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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305H HIS* 4.8 0.5 - - - -
322H LYS* 4.1 9.2 - - - -
323H SER 4.4 3.3 + - - -
325H GLU* 3.2 11.1 + - + +
326H ASN* 1.3 81.1 - - - +
328H ILE* 1.3 61.6 + - - +
329H VAL* 3.6 11.6 + - + +
355H ARG* 4.3 22.2 - - + +
356H PHE 3.2 18.8 - - - +
357H ASP* 4.2 9.4 - - - +
358H TYR* 3.2 15.5 + - - -
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Residues in contact with ILE 328 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320H LEU* 4.1 19.7 - - + -
321H SER 3.7 15.5 - - - +
322H LYS* 4.1 12.3 - - + -
327H ALA* 1.3 69.8 - - - +
329H VAL* 1.3 60.9 + - - +
356H PHE* 2.9 43.7 + - + +
358H TYR* 3.4 14.1 - - + -
368H PHE* 3.7 37.5 - - + -
377H LEU* 3.9 28.0 - - + -
379H LEU* 4.0 8.5 - - + -
389H TRP* 4.0 16.8 - - + -
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Residues in contact with VAL 329 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304H ILE* 4.3 3.6 - - + +
305H HIS* 4.0 18.8 - - + +
319H ILE 3.2 5.5 - - - +
320H LEU* 3.3 3.3 - - - -
321H SER 2.8 36.5 + - - +
325H GLU* 5.1 4.3 - - - +
327H ALA* 3.9 12.6 - - + +
328H ILE* 1.3 73.1 - - - +
330H CYS* 1.3 65.7 + - - +
331H TRP* 3.5 10.3 - - + -
352H ILE* 3.7 34.1 - - + -
354H GLY 3.6 13.9 - - - +
355H ARG* 4.3 24.7 - - + +
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Residues in contact with CYS 330 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42G PHE* 3.8 20.2 - - + -
315H LEU* 3.9 11.0 - - + -
318H LEU* 3.7 39.3 - - - -
319H ILE 3.2 5.6 - - - -
320H LEU* 3.7 14.7 - - + +
328H ILE 3.8 3.2 + - - -
329H VAL* 1.3 71.0 - - - +
331H TRP* 1.3 56.2 + - - +
352H ILE 3.8 0.3 - - - -
353H LEU* 2.8 31.4 + - - -
354H GLY* 3.0 21.9 + - - +
356H PHE* 4.6 9.1 - - + -
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Residues in contact with TRP 331 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H MET* 4.4 7.6 - - + -
260H LEU* 3.6 34.5 - - + -
299H PHE* 3.9 23.3 - + - -
301H THR* 4.3 3.4 - - + -
304H ILE* 3.4 39.6 - - + +
318H LEU* 3.8 5.5 - - - +
319H ILE* 2.8 66.2 + - + +
321H SER* 2.8 22.6 + - - -
329H VAL* 3.5 12.6 - - + -
330H CYS* 1.3 74.4 - - - +
332H LYS* 1.3 88.1 + - - +
333H PRO* 3.8 18.8 - - + -
350H VAL* 4.2 5.6 - - + -
351H THR 3.1 15.5 - - - +
352H ILE* 3.9 9.4 - - + -
353H LEU* 4.0 4.3 - - - +
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Residues in contact with LYS 332 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41G MET* 3.9 14.9 - - + +
317H ASP 5.0 2.5 - - - +
318H LEU* 3.8 25.1 - - + -
319H ILE 5.0 0.7 - - - +
331H TRP* 1.3 86.1 - - - +
333H PRO* 1.4 83.0 - - + +
335H LYS 3.8 4.4 + - - +
336H MET* 2.9 40.7 + - + +
337H GLU 4.3 0.4 - - - -
338H ASP 2.6 31.3 + - - -
339H ASP* 5.0 0.2 - - - +
340H ILE* 5.4 4.7 - - - +
350H VAL* 3.4 3.8 - - - +
351H THR* 2.8 49.6 + - - +
353H LEU* 4.3 4.5 - - + -
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Residues in contact with PRO 333 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252H MET* 4.6 8.5 - - + -
299H PHE* 3.6 49.8 - - + -
317H ASP 5.1 2.9 - - - +
319H ILE* 4.6 8.1 - - + -
331H TRP* 4.0 8.1 - - + -
332H LYS* 1.4 101.3 - - + +
334H GLY* 1.3 59.2 + - - +
338H ASP 4.1 3.6 - - - +
340H ILE* 3.6 27.6 - - + +
343H ILE* 3.6 23.6 - - + +
349H ASN 4.1 0.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il